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Coding Skills

R
Python
Bash
AWK
SQL
Perl

R: tidyverse, data.table, Shiny, plotly, tidymodels, caret and others
Python: NumPy, Pandas, SciPy, scikit-learn, keras, PyTorch, Seaborn, matplotlib and more

Languages

Polish
English
French

Disclaimer

CV source code. Made with pagedown, based on nstrayer/cv.

Last updated on 2022-11-30.

Main

Kasia Kedzierska

I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. My work includes data exploration, data visualisation and communicating results to non-technical audience. For example, I take advantage of feature selection and dimensionality reduction methods, generate hypothesis with unsupervised learning and test them with in silico and in vitro experiments. I model complex biological processes with a repertoire of ML models - from Linear Models to Deep Learning.

Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I worked with NLP methods and knowledge graphs. Currently, I am looking into adapting my experience from the internship to build models investigating cancer evolution.

Selected Work Experience

Intern @ Novo Nordisk Research Centre Oxford, Oxford, United Kingdom

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2021

  • I used NLP based methods to screen biomedical articles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.

DPhil Candidate @ Wellcome Centre for Human Genetics, Big Data Institute, University of Oxford, UK

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N/A

present - 2018

  • In my PhD project Functional and evolutionary characterisation of chromatin organisation in endometrial cancer I am looking at how chromatin organisation influences disease progression in cancer of the uterus.
  • Currently I’m working on building and refining ML models of cancer evolution.

Visiting Graduate Student @ Ratan group, University of Virginia, USA

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N/A

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Education

DPhil. Candidate, Genomic Medicine and Statistics @ Nuffield Department of Medicine, Brasenose College, University of Oxford, UK

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present - 2018

M. Sc. Eng., Biotechnology @ Warsaw University of Technology, Warsaw, Poland

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2018 - 2015

  • Master thesis: - Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.

Selected Awards and Honors

Senior Hulme Scholarship

Brasenose College, University of Oxford

Oxford, UK

present - 2021

  • Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.

Graduate Prize in the ‘Outstanding work outside degree’ category

Nuffield Department of Medicine, University of Oxford

Oxford, UK

2022 - 2021

  • Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College London

London, United Kingdom

2019

Selected Publications

Full list of publication is available through my Google Scholar profile scholar.google.com/citations?user=Yv6poTwAAAAJ.

Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift @ BMC Genomics

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2021

M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability @ Clinical Epigenetics

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2020

H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development @ Genome Research

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2019

M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata

SONiCS: PCR stutter noise correction in genome-scale microsatellites @ Bioinformatics

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N/A

2018

K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler

Selected Conference Presentations

Poster presentation: Systematic characterisation of chromatin modifiers in endometrial cancer @ European Association for Cancer Research 2022 Congress

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2022

Invited talk: Analysis of the mutational burden across gene sets in cancer @ Polish Bioinformatics Society Symposium

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2019

Poster: Differential mutation analysis across gene sets in cancers @ Biology of Genomes 2018

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N/A

2018

Teaching Experience

Unsupervised learning @ NGSchool2022: Machine Learning in Computational Biology

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2022

Data visualization in bioinformatics - hackathon mentor @ Online hackathon NGSprint

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2021

Online tutorials: Python for Data Science and Introduction to Python @ NGSeminars

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2020

Introduction to R @ Wellcome Centre for Human Genetics

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2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

Introduction to Managing Code with Git @ Wellcome Centre for Human Genetics

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N/A

2020 - 2019

Selected Grants

Visegrad Grant to organize NGSchool2022 @ Visegrad Fund

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2022 - 2020

  • 32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of volunteers and led the organisation of summer school, conference, online seminars and hackathon.

Non-profit Work

President @ NGSchool Society

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N/A

present - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019, Founder